Prunier received a PhD in African History in 1981 from the University of Paris. In 1984, he joined the CNRS scientific institution in Paris as a researcher. He later also became Director of the French Centre for Ethiopian Studies in Addis Ababa.
Prunier has published over 120 articles and five books. He is fluent in his native French, as well as English and Spanish. He also has good knowledge of Italian and German, and a basic knowledge of Juba Arabic (Sudanese colloquial Arabic) and Swahili.
- (in French) Les Ethnies ont une histoire (ed. with Jean-Pierre Chrétien), Paris : Karthala, 1989, ISBN 2-86537-226-X
- (in French) L'Ouganda et la question indienne : 1896-1972, Paris : Editions Recherche sur les civilisations, 1990
- The Rwanda Crisis: History of a Genocide, Columbia University Press, 1995, ISBN 0-231-10408-1
- (in French) Le Kenya contemporain, (ed. with François Grignon), Paris : Karthala & Nairobi : IFRA, 1998, ISBN 2-86537-793-8
- Darfur: The Ambiguous Genocide, Cornell University Press, 2005, ISBN 0-8014-4450-0
- L'Éthiopie contemporaine (director), CFEE-Karthala, Addis Abeba and Paris, 2007, ISBN 978-2-84586-736-9
- From Genocide to Continental War: The "Congolese" Conflict and the Crisis of Contemporary Africa, C. Hurst & Co., 2009, ISBN 1-85065-523-5
- "Burundi: A Manageable Crisis?", WRITENET (UK), October 1994
- "Sudan’s regional war", Le Monde diplomatique, February 1997 (in English)/(in French)
- "Rwanda: the Social, Political and Economic Situation", WRITENET (UK), June 1997
- "Somaliland, a forgotten country", Le Monde diplomatique, October 1997 (in English)/(in French)
- "Uganda, nearly a miracle", Le Monde diplomatique, February 1998 (in English)/(in French)
- "Somalia re-invents itself", Le Monde diplomatique, April 2000 (in English)/(in French)
- "Sudan: irreconcilable differences, Le Monde diplomatique, December 2002 (in English)/(in French)
- "Did Somebody Say Genocide?: Gérard Prunier on Darfur", Harper's Magazine, August 2006
- "Darfur's Sudan problem", opendemocracy.net, 15 September 2006
- The Ethio-Eritrean Conflict: An Essay in Interpretation
- Armed Movements in Sudan, Chad, CAR, Somalia Eritrea and Ethiopia
- Somalia: Civil War, Intervention and Withdrawal 1990 - 1995
- From Fatigues to Three-Piece Suits: East African Guerrillas in Power
- Why did South Sudan blow up in December 2013 and what is likely to happen as a result?
- Fergal Keane, Interview of Prunier on the Rwandan Genocide, PBS's Frontline (early 1997)
- Gerard Prunier on 'la francophonie' under threat at Just World News blog with Helena Cobban, 31 May 2004
- Prunier, Gérard (2008-12-22). "Curriculum Vitae" (PDF). International Criminal Court at The Hague. Retrieved 15 June 2013.
- Articles by Prunier at openDemocracy
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